SFG2

Survival Forest Graphs for Overall Population and by Percentiles of Continuous Biomarker

SFG

We prepare the data similarly as in SFG1. In particular we use again the cut_quantile_bins() function, here to obtain quartile bins of the continuous biomarker BMRKR1.

Code

library(tern)
library(dplyr)

BMRKR1_probs <- c(0.25, 0.5, 0.75)

adtte <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(
    PARAMCD == "OS"
  ) %>%
  mutate(
    AVAL = day2month(AVAL),
    AVALU = "Months",
    is_event = CNSR == 0,
    ARM_BIN = fct_collapse_only(
      ARM,
      CTRL = c("B: Placebo"),
      TRT = c("A: Drug X", "C: Combination")
    ),
    BMRKR1 = ifelse(BEP01FL == "N", NA, BMRKR1),
    BMRKR1_BIN = explicit_na(cut_quantile_bins(BMRKR1, BMRKR1_probs)),
    BMRKR2 = fct_explicit_na_if(BMRKR2, BEP01FL == "N")
  ) %>%
  var_relabel(
    BEP01FL = "BEP",
    BMRKR2 = "Biomarker (Categorical)",
    BMRKR1_BIN = "Biomarker (Binned)"
  )

For the calculations, we start by getting the levels from BMRKR1_BIN which saves us typing them manually in the groups_lists definition. This definition is required here so that we can have overlapping subgroups.

Code

BMRKR1_BIN_levels <- levels(adtte$BMRKR1_BIN)

tbl <- extract_survival_subgroups(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM_BIN",
    subgroups = c("BEP01FL", "BMRKR1_BIN")
  ),
  label_all = "ITT",
  groups_lists = list(
    BMRKR1_BIN = list(
      "(25%,100%]" = BMRKR1_BIN_levels[2:4],
      "(50%,100%]" = BMRKR1_BIN_levels[3:4],
      "(75%,100%]" = BMRKR1_BIN_levels[4]
    )
  ),
  data = adtte
)

result <- basic_table() %>%
  tabulate_survival_subgroups(
    df = tbl,
    vars = c("n_tot_events", "n", "n_events", "median", "hr", "ci"),
    time_unit = adtte$AVALU[1]
  )

We can now produce the forest plot using the g_forest() function from tern based on this result table.

Code

g_forest(result)

Code

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.1.4      tern_0.9.5       rtables_0.6.9    magrittr_2.0.3  
[5] formatters_0.5.9

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0             gtable_0.3.5             jsonlite_1.8.8          
 [4] compiler_4.4.1           tidyselect_1.2.1         stringr_1.5.1           
 [7] tidyr_1.3.1              splines_4.4.1            scales_1.3.0            
[10] yaml_2.3.10              fastmap_1.2.0            lattice_0.22-6          
[13] ggplot2_3.5.1            R6_2.5.1                 labeling_0.4.3          
[16] generics_0.1.3           knitr_1.48               forcats_1.0.0           
[19] rbibutils_2.2.16         htmlwidgets_1.6.4        backports_1.5.0         
[22] checkmate_2.3.2          tibble_3.2.1             munsell_0.5.1           
[25] pillar_1.9.0             rlang_1.1.4              utf8_1.2.4              
[28] broom_1.0.6              stringi_1.8.4            xfun_0.47               
[31] cli_3.6.3                withr_3.0.1              Rdpack_2.6.1            
[34] digest_0.6.37            grid_4.4.1               cowplot_1.1.3           
[37] lifecycle_1.0.4          vctrs_0.6.5              evaluate_0.24.0         
[40] glue_1.7.0               farver_2.1.2             codetools_0.2-20        
[43] survival_3.7-0           random.cdisc.data_0.3.15 fansi_1.0.6             
[46] colorspace_2.1-1         purrr_1.0.2              rmarkdown_2.28          
[49] tools_4.4.1              pkgconfig_2.0.3          htmltools_0.5.8.1

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